seems to me like your code snippet will damage a file where ^M are already missing: chomp will remove \n and chop next to it will eat a good character.

Secondly, it will not work on Win32, because you did not used "binmode" on that filehandle.

Additionally I just thought about not important but funny thing: you closed a filehandle because it is a good practice (perldoc says that it's not needed, because perl does this for you).
Let's go further and do even more: let's undefine all defined wariables, return to initial directory, and so on...
:)

Courage, the Cowardly Dog.